If you mean the original .rgn, no there is no difference if you flash it simply by Updater.exe or with cure program.
You should try to format your device, probably there is something else causing the problem.
Backup all on pc and format it with RMPrepUSB (FAT 32)
[Only registered and activated users can see links. ]
reflash original firmware, add garmindevice,xml in a Garmin folder , run Webupdater and restart it to see if it starts normally, then you can try to add missing files one by one from backup. But caution with files might brick it again.